[Freesurfer] SynthSR

2022-10-07 Thread AJ 
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Can SynthSR be used on MRI scans of subjects with T2 lesions, such as MS?
If yes, is their a way to save the masks of lesions that were Inpainted or
their volume?


For the output files, what are their image parameters such as TR, TE, TI?


Thank you,
AJ
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[Freesurfer] fft

2022-10-07 Thread Proulx, Jean Sebastien 
Hello,

Is there an easy way to perform fast fourier transform (fft) or other fancier 
spectral analysis with freesurfer tools (e.g. with mris_calc)?

Thanks and
Have a good day!
Sebastien
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Re: [Freesurfer] Hemisphere in Yellow

2022-10-07 Thread Wang, Ruopeng 
Would it be possible to send me the overlay file?

On Oct 7, 2022, at 1:27 PM, Jun Yeon Won mailto:wo...@umd.edu>> 
wrote:


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Hi  Ruopeng,

I tried to adjust overlay thresholds in the Configure Overlay window, but I 
think it still looks weird. The gray part should be blue and the blue part 
should be gray since when I clicked the gray part it showed -1.6 and the blue 
0. Could you please let me know how to flip this?



I also tried to overlay annot file according to the instruction on this page 
(MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis)
 using the below script.

freeview -f 
$SUBJECTS_DIR/fsaverage/surf/rh.inflated:overlay=cache.th20.abs.sig.cluster.mgh:overlay_threshold=2,5:annot=cache.th20.abs.sig.ocn.annot
 -viewport 3d



So this result shows the gray part in the first photo should be blue. Could you 
please advise?

Best,
Jun

On Thu, Oct 6, 2022 at 4:38 PM Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>> wrote:
You can adjust overlay thresholds in Configure Overlay window.

Ruopeng

On Oct 6, 2022, at 10:49 AM, Jun Yeon Won mailto:wo...@umd.edu>> 
wrote:


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Dear Freesurfer experts,

I am running a linear regression analysis and found a significant result 
showing below (cache.th20.abs.sig.cluster.summary file).


I ran the below script to get this result. Right hemisphere was focused for 
this analysis.

  mri_glmfit-sim --glmdir rh.thickness.10.glmdir \
  --cache 2 abs \
  --cwp 0.05


But, when visualizing the cache.th20.abs.sig.cluster.mgh file, it shows below - 
the hemisphere is in yellow.



The below is a visualization of sig.mgh. The underlay should be gray but I am 
not sure why the underlay looks yellow when overlaying the thresholded result.



 I saw somebody posted the same issue here (MailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to be 
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg46328.html),
 but I was not able to find the solution from here.  Could you please let me 
know what is an issue and how to resolve this?

Best,
Jun

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[Freesurfer] Specify random seed with recon-all

2022-10-07 Thread Elizabeth Kenneally 
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Hi FreeSurfer Developers,

I’m trying to run FreeSurfer with a specified random seed with recon-all. I 
found the -rng-seed flag, but it seem to have been deprecated. I also found the 
-randomness flag, but I was hoping to specify the random seed myself for 
testing purposes. Is there a way to do this in the newer versions? I searched 
the mail archives and didn’t find anything recent.

Version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Platform: OSX Monterey

Thanks for your help!


Elizabeth Kenneally
Assistant Research Engineer
Computational Neuroimaging Laboratory

Child Mind Institute
917.472.1812
childmind.org
  |  
Location
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[Freesurfer] Parcellating Individuals using Yeo17Networks Atlas

2022-10-07 Thread Remiszewski, Natalie 
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Hi all,

I have a dataset of structural MRIs that I have previously used FS on to 
parcellate into the DKT and Destrieux atlases. I am interested in parcellating 
and getting cortical thickness values using the yeo17networks atlas. Is there a 
way to modify recon-all so that i can get individual yeo17 data for each 
subject? Thank you!


Best,


Natalie Remiszewski

Graduate Student Trainee

University of Alabama at Birmingham

Kraguljac Lab

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Re: [Freesurfer] Freeview does not show images

2022-10-07 Thread fsbuild 
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Did it say the driver was installed successfully?  I’m wondering if the 
driver did not install because it does not support your machines hardware for 
some reason. But it should tell you if it cannot be installed.

You can tell if the DCH driver is installed by following the instructions 
here,https://secure-web.cisco.com/1C5iHX14FwFkb0bd5IYlzilnGkZNKBRhHFB5E1e8VAvgm832QpAA9pmst0ZQuoC01uGEtlN0Qfoy-8iUOVAv0r83MvIFhsS80-v9aycte39pSTISKdutTDgKy-hUW2qUx7xQZlC_l0pzPpONAt9fSyazQZ1GnRIQAMDEESUBRNX0c-v5cahiYmnyhb-nCV1r0ZvrgDZ7ghyZbtWcGndQw6amYiwjrvnXcDvAMEq5qd7pU3QU8ZOl9LnfFOQ6-k-ZLWIW6e0Yi8IRtVSlJSwNiDgACgB4gBvastg8A-sPy18j6Cfqj7NAY_DRglVfDj6Q80iOZn7cNsef3V1nq15s3WA/https%3A%2F%2Fwww.intel.com%2Fcontent%2Fwww%2Fus%2Fen%2Fsupport%2Farticles%2F58296%2Fgraphics.html
There is more info about it 
here,https://secure-web.cisco.com/1OnUvmRVhRWfRd2WCZXsandn42tB-a7ROvNPXbkZSl_hqHPKINKCSHkLxTmBG52oxmFqNtZjYTJ4Ppsay9_RddV5-RNszenkWzdmp4HV-k_JjuxpBLReMrMuOZL81oKe1VYne_9XcnTCtTbwzqyk6E5zeTXMOjQLj9-LeBN1OjCg16d38W4e9brBF4IQ4m5PdQjQQKLE5dak8O_fvzZ6AbMssGWmc3vnGyQFRuvfHgDq6SzzD5T2doFTIUemiQkSfxIMt4N5QyFpPyk5A1dbQcglJ1XctZd5C9TUn8KHtL_PYtauBGmPBHy7agS-rlu3q/https%3A%2F%2Fwww.intel..com%2Fcontent%2Fwww%2Fus%2Fen%2Fsupport%2Farticles%2F58295%2Fgraphics.html
- R.
On Oct 7, 2022, at 06:05, Justina Lee justinale...@gmail.com 
wrote:External Email - Use 
CautionHi Ruopeng,I tried 
to run the glxgears command in the WSL Ubuntu subsystem, but it doesn't show me 
the gears. I am having the same issue as this thread linked 
here:MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to 
behttps://secure-web.cisco.com/1NxVL-emVuHw_jOzG4gXfcbpKLhoo9hS4C5IwCTkrb4Ge9RJeQgNfYxUY1b8UhVCwRwafISyQbYMLx5-0RvvSU6ZggG_ziHWkZu0dtETp0bWIPD2HpbN6cd9K0jyPv1EBAwomGF2psP-nMqtKFGOakonOE6Q_h5y-kwI5W6pz9NkKkFvaiUlrprN5Kw4EXmO6JNwQEEw8dt3jPlAlFb2GTb8v7sMcKcBtvKJX5-yZ1wcnQudjQkqYOv4-1MPtgi-cUNyFr_ZXvY5rkay6B-wM9gX5K9w7EmXiyuHWMwtAcDEuN9kXbDMGWjIX1ffOkkcs218lhqcGDyQ2a1ZisDYd_w/https%3A%2F%2Fgithub.com%2Fmicrosoft%2Fwslg%2Fissues%2F654
 I followed the advice and downloaded the latest Intel Graphics Driver, but 
this did not seem to fix the issue for me.I also looked at the 
corresponding debian package installer in accordance with my ubuntu version, 
and the same error occurs. How can I add a 3D accelerator or GPU acceleration 
so that the glxgears command can show me the gears?Thanks for your help and 
time.Sincerely,JustinaOn Thu, Oct 6, 2022 at 3:39 PM Wang, Ruopeng 
rwa...@mgh.harvard.edu wrote:Are you able to run glxgears command? Do 
you see spinning gears?RuopengOn Oct 6, 2022, at 4:28 AM, Justina Lee 
justinale...@gmail.com 
wrote:External Email - Use 
CautionTo whom this may concern 
and can help,I am currently trying to run Freeview under the 
WindowsSubsystem Linux System. I can successfully download and open 
images, but nothingseems to be showing onmy end (see image attached 
at the end).In order to find out what is preventing the X-server from 
correctly displaying graphics, I have tried to run the $ xeyes command and the 
eyes pop up, meaning that the X-windows server is working fine.Upon checking 
the WSL Version, I am currently using the WSL version 2.I have entered the two 
commands as follows:$echo "export XDG_RUNTIME_DIR=$HOME/.xdg"  
$HOME/.bashrc$echo "export DISPLAY=:0"  $HOME/.bashrcThen I 
exited Ubuntu, and tried to run freeview again (attempting to open a data file 
T1.mgz.) This still did not produce any image in freeview, although it opened 
it up. I tried changing the window, contrast, and brightness but to no 
avail.Is there another solution?Terribly sorry and thank you so much for 
your time.Sincerely,JustinaFreeview image 
display.png___Freesurfer 
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Re: [Freesurfer] Freeview does not show images

2022-10-07 Thread Justina Lee 
External Email - Use Caution

Hi  Ruopeng,

I tried to run the glxgears command in the WSL Ubuntu subsystem, but it
doesn't show me the gears. I am having the same issue as this thread linked
here: 
https://secure-web.cisco.com/1_nwpKy6edOMjc8Fb4TT_DQsKayIHq7yz6rjZXWYrhXvOMtkPtnDTAgvyHwlJknIz0NqjN44E48l9HTzHWpxTRB7K9qfWEddgLzY-N8DwQ9LJuanknR3cqBZCSGGybx3kfCwXL0JqnlBMKd4YPRiOBQ0tvJnklmkeHvAu0bOaW_5y3ABUG-9zqwhYo-JKOs-npIB2AdvV4eRkQ6-M0I8iPV2U8PHw1JoFhE100pzdpkEHDewV_Z7VJaoHYTWjJR4LPr_DMg2vecc2aM_SIu4Zgmk3bNNQ0II7UXChxgZatN8b6T1b4ayMSM8cKseJiDTbEG_czfPEz8ArXDVdM5yDMQ/https%3A%2F%2Fgithub.com%2Fmicrosoft%2Fwslg%2Fissues%2F654
 I followed the advice
and downloaded the latest Intel Graphics Driver, but this did not seem to
fix the issue for me.

I also looked at the corresponding debian package installer in accordance
with my ubuntu version, and the same error occurs. How can I add a 3D
accelerator or GPU acceleration so that the glxgears command can show me
the gears?

Thanks for your help and time.

Sincerely,
Justina

On Thu, Oct 6, 2022 at 3:39 PM Wang, Ruopeng  wrote:

> Are you able to run glxgears command? Do you see spinning gears?
>
> Ruopeng
>
> On Oct 6, 2022, at 4:28 AM, Justina Lee  wrote:
>
> External Email - Use Caution
>
> To whom this may concern and can help,
>
> I am currently trying to run Freeview under the Windows Subsystem Linux
> System. I can successfully download and open images, but nothing seems to
> be showing on my end (see image attached at the end).
>
> In order to find out what is preventing the X-server from correctly
> displaying graphics, I have tried to run the $ xeyes command and the eyes
> pop up, meaning that the X-windows server is working fine.
>
> Upon checking the WSL Version, I am currently using the WSL version 2.
>
> I have entered the two commands as follows:
>
> $ *echo "export XDG_RUNTIME_DIR=$HOME/.xdg" >> $HOME/.bashrc*
> $ *echo "export DISPLAY=:0" >> $HOME/.bashrc*
> Then I exited Ubuntu, and tried to run freeview again (attempting to open
> a data file T1.mgz.) This still did not produce any image in freeview,
> although it opened it up. I tried changing the window, contrast, and
> brightness but to no avail.
>
> Is there another solution?
>
> Terribly sorry and thank you so much for your time.
>
> Sincerely,
> Justina
> 
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